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Analytical Chemistry

Let’s Just Braille Out That Chemical Structure, Shall We?


Atomic force microscopy, a technique that has given us images of individual atoms and molecules, has racked up another success. A collaboration between the IBM-Zürich group (who have done so much in this area) and a group at the University of Santiago de Compostela (in Spain) has determined the structure of a reactive intermediate, and it’s not what one would have thought.

They’re working from a di-iodo derivative of the flat structures shown, and that turns into what can be variously drawn as a diradical (at top), an aryne (in the middle) or a cumulene (at bottom). You can change one into another by just moving electrons around, but the real species is probably a lot more like just one of them: but which one? This is not an easy question to answer by traditional physical organic chemistry, at least at this level of detail, but what if you could just reach down, pluck the iodines off a single molecule, and look at the result?

AFM aryne

That’s the bizarre question that AFM lets you ask. The microscope tip (at high voltage) was used to break the iodo bonds, and then the isolated molecule was imaged (shown). Comparing bond lengths and angles, it looks a lot more like a cumulene than the other alternatives. It’s possible that being adsorbed onto a surface alters things as compared to a solution reaction, but under these conditions, a cumulene is apparently what you get.

And as that Chemistry World article says, this same technique can now be used for many other mechanistic questions. For those of us who grew up, scientifically, with mental pictures of fleeting reactive intermediates, things that could only be speculated on by watching the indirect evidence they leave behind. . .well, this is a bit spooky. But AFM images have always had that effect on me. Eventually, this will come to seem normal. And I wonder how far that will go? Can atomic force microscopy ever become a standard analytical technique – want to know a structure, just run the AFM tip over it? We’re a long way from that now (you’ll notice that the great majority of these sorts of papers come from just that IBM lab), but ruling out advances instrumentation is not the way to bet. I’m not expecting a walk-up instrument any time soon, but this looks like far too useful and powerful a technique to keep down for too long.

16 comments on “Let’s Just Braille Out That Chemical Structure, Shall We?”

  1. Old man says:

    Your middle structure seems to have 4 hydrogen atoms in the ring on the right, while the other two structures would seem to have only two hydrogens on that ring. Perhaps the middle structure should have single electrons at the two “benzylic” positions to be at the same overall oxidation state?

  2. Resonymous says:

    Agreed with #1. There are some charges missing in the middle structure. The number of pi electron should remain constant.

  3. ER says:

    AFM is a great tool for imagining molecules… if they’re flat. Otherwise not so much. I suspect that you’d get a solid blob if you tried this with anything non-planar.

  4. if you would like to watch a video with the authors of the paper explaining their technique check this out:

  5. #3: 3D AFM doesn’t sound that far fetched to me in the near future.

  6. Derek Lowe says:

    Right you are about the pi bonds – I’ve changed them to the weasely dotted lines so as not to draw them as two localized double bonds.

  7. David Stone says:

    The Chemistry World announcement linked right at the top of the article shows a couple of = on that ring. I think Derek’s version is an artefact of the way the aromatic rings were orientated when drawn.
    Here’s a direct link to the original figure for comparison – note the positions of the = on the fused aromatic rings:

  8. David Stone says:

    @6 Derek, @1 and @2 were referring to the alkyne structure (middle), not the cumulene (bottom)

  9. Derek Lowe says:

    Ah, gotcha. I’ve fixed the bonding on the aryne, too – should show up momentarily on the published page.

  10. Check it out, Nature Chemistry selected the aryne paper for the August issue COVER:

  11. Anonymous says:

    Before even reading this post and looking at the results, I figured the cumulene structure would be predominant simply due to the greater entropy of a more delocalized electron system.
    Delocalized systems are *always* the predominant species provided they do not significantly disrupt the atomic geometry.

  12. Nick K says:

    #2,9: Sorry, could you explain?. I don’t see the problem with the cumulene being drawn with three discrete double bonds. The middle double bond is orthogonal to the other two, and is thus not involved in the aromatic sextet.

  13. Anonymous says:

    Ahhhhhh…… models…..

  14. Anonymous says:

    #12: There isn’t a problem with discrete double bonds (it’s what they do in the paper). Drawing the dotted lines is misleading as it suggests the orthogonal pi-bond is conjugated.
    #11: Are you suggesting that for arynes the cumulene form should predominate generally? Both resonance structures are aromatic.

  15. Paul D. says:

    Ars Technica UK has a story on the ultra-quiet rooms IBM/ETH have built to operate AFMs and such:
    Apparently the strict attention to noise reduction can improve the resolution of these devices by a factor of 2-3, which is huge.

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